Qingshengii Strain Research Articles

Rhodococcus qingshengii GlMm1 as the Basis of a Biosensor for Determination of the Fungicide Carbendazim

The possible application of Rhоdococcus qingshengii strain GlMm1, isolated from a Dead Sea clay sample, as the basis of a biosensor for determining the benzimidazole fungicide carbendazim was investigated. High sensitivity of the biosensor under neutral pH and up to 500 mM NaCl at 2 to 160 μM carbendazim was maintained for up to 30 days.

Potential of the plant growth-promoting rhizobacterium Rhodococcus qingshengii LMR356 in mitigating lead stress impact on Sulla spinosissima L.

Mining-related lead (Pb) pollution of the soil poses serious hazards to ecosystems and living organisms, including humans. Improved heavy metal phytoremediation efficacy, achieved by using phytostabilizing plants assisted by plant-growth-promoting (PGP) microorganisms, has been presented as an effective strategy for remediating polluted soils. The objective of this research was to examine the response and potential of the plant-growth-promoting bacterium LMR356, a Rhodococcus qingshengii strain isolated from an abandoned mining soil, under lead stress conditions. Compared to non-contaminated culture media, the presence of lead induced a significant decrease in auxin production (from 21.17 to 2.65 μg mL-1) and phosphate solubilization (from 33.60 to 8.22 mg L-1), whereas other PGP traits increased drastically, such as 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity (from 38.17 to 71.37 nmol mg-1 h-1 α-ketobutyrate), siderophore production (from 69 to 83%), exopolysaccharide production (from 1952.28 to 3637.72 mg mL-1), biofilm formation, and motility. We, therefore, investigated the behavior of Sulla spinosissima L. in the presence or absence of this strain under a variety of experimental conditions. Under hydroponic conditions, Sulla plants showed endurance to varying lead concentrations (500-1000 μM). Inoculation of plants with Rhodococcus qingshengii strain LMR356 enhanced plant tolerance, as demonstrated by the increase in plant biomass (ranging from 14.41 to 79.12%) compared to non-inoculated Pb-stressed and non-stressed control plants. Antioxidant enzyme activities (increasing by -42.71 to 126.8%) and chlorophyll (383.33%) and carotenoid (613.04%) content were also augmented. In addition to its impact on plant lead tolerance, strain LMR356 showed a growth-promoting effect on Sulla plants when cultivated in sterilized non-contaminated sand. Parameters such as plant biomass (16.57%), chlorophyll (24.14%), and carotenoid (30%) contents, as well as ascorbate peroxidase (APX), peroxidase (POD), and catalase (CAT) activities, were all elevated compared to non-inoculated plants. Furthermore, when the same plant species was cultivated in highly polluted soil, inoculation increased plant biomass and improved its physiological properties. These findings demonstrate that LMR356 is a phytobeneficial bacterial strain capable of enhancing Sulla growth under normal conditions and improving its heavy metal tolerance in multi-polluted soils. Thus, it can be considered a promising biofertilizer candidate for growing Sulla spinosissima L. or other selected plants intended for application in restoration and stabilization initiatives aimed at reviving and safeguarding environmentally compromised and polluted soils after mining activities.

Detection of gene clusters for biodegradation of alkanes and aromatic compounds in the Rhodococcus qingshengii VKM Ac-2784D genome.

Bacterial species of the genus Rhodococcus are known to be efficient degraders of hydrocarbons in contaminated soil. They are also employed for bioremediation of polluted environments. These bacteria are widely met in soil, water and living organisms. Previously, we have isolated the Rhodococcus qingshengii strain VKM Ac-2784D from the rhizosphere of couch grass growing on oil-contaminated soil. This strain can effectively degrade oil and some model compounds (naphthalene, anthracene and phenanthrene). The results of phylogenetic analysis show that this strain belongs to the species R. qingshengii. To understand the catabolic properties of this strain, we have studied its gene clusters possessing such properties. The alkane destruction genes are represented by two clusters and five separate alkB genes. The destruction of aromatic compounds involves two stages, namely central and peripheral. The R. qingshengii VKM Ac-2784D genome contains four out of eight known central metabolic pathways for the destruction of aromatic compounds. The structure of the gene clusters is similar to that of the known strains R. jostii RHA1 and R. ruber Chol-4. The peripheral pathways include the genes encoding proteins for benzoic acid destruction. The presence of biphenyl 2,3-dioxygeneses as well as gene clusters of benzoate and 2-hydroxypentandienoate pathways suggests that R. qingshengii VKM Ac-2784D could degrade polychlorinated biphenyls. The biodegradation ability can be enhanced by biosurfactants, which are known to be synthesized by Rhodococcus. The R. qingshengii VKM Ac-2784D genome contains the otsA, otsB, treY, treZ genes. The bioinformatics data are supported by the previous biochemical experiments that allow a mixture of species with a wide variation of metabolic pathways to be obtained.

Complete Genome Sequence of Rhodococcus qingshengii Strain PM1, Isolated from a Selenium-Rich Mine in China.

Rhodococcus qingshengii PM1 was isolated from selenium-rich carbonaceous mudstones in Enshi, Hubei, China. Here, we report the complete genome sequence of this strain, which was obtained by combining Illumina and Nanopore sequencing.

Physiological and biochemical characterization and genome analysis of Rhodococcus qingshengii strain 7B capable of crude oil degradation and plant stimulation

Rhodococci are typical soil inhabitants which take part in remediation of soil polluted with hydrocarbons. In this paper, we describe a new strain, Rhodococcus qingshengii 7B, which is capable of growth and hydrocarbon degradation at 45°C and in the presence of up to 10% NaCl in the medium. The genome of the 7B strain consists of a 6,278,280 bp chromosome and two plasmids. The circular plasmid is 103,992 bp in length. The linear plasmid is 416,450 bp in length. Genome analysis revealed the genes of degradation of various hydrocarbons, resistance to salt stress and plant growth promoting activity. This strain is promising for use in remediation of oil-contaminated soils, because it has a pronounced ability to utilize crude oil, oil sludge and individual hydrocarbons in a wide temperature range. Over 15 days of the experiment, the strain utilized 51% of crude oil at 28°C and 24% at 45 °С.

Native Heavy Metal-Tolerant Plant Growth Promoting Rhizobacteria Improves Sulla spinosissima (L.) Growth in Post-Mining Contaminated Soils.

The potential of rhizobacteria in assisting plants used in the phytostabilization or re-vegetation of soils contaminated by heavy metals is gaining interest all around the world. In this context, six rhizobacterial strains isolated from highly heavy metal-contaminated soils situated in abandoned mining sites around the Oujda region (Morocco) were tested with Sulla spinosissima (L.), a native leguminous plant expanding in this area. The strains used were multi-resistant to heavy metals and possessed multiple plant growth-promoting traits. Potential beneficial effects of the strains were also evaluated in planta by measuring various growth and physiological parameters of inoculated Sulla plants grown in sterilized sand. Inoculation with the Rhodococcus qingshengii strain LMR340 boosted plant biomass (39% to 83% increase compared to uninoculated plants), chlorophyll and carotenoid content (up to 29%), and antioxidant enzyme activities (15% to 80% increase). Based on these interesting findings, selected strains were inoculated into plants growing in a heavy metal, multi-polluted, and poor soil. Under these conditions, non-inoculated plants and those inoculated with the strain LMR250 were unable to grow, while the other five bacterial inoculants restored plant growth. The best performing strain, Pseudarthrobacter oxydans LMR291, could be considered as a good biofertilizer and/or biostimulant candidate to be used for promoting the growth of selected plants in re-vegetation and/or phytostabilization programs of degraded and contaminated soils.

Draft Genome Sequence of Rhodococcus qingshengii (Formerly erythropolis) TA37, a First-Generation Biocatalyst for Synthesis of Functionalized Acrylamides.

ABSTRACTWe describe here the 7.0-Mb draft genome sequence of Rhodococcus qingshengii strain TA37, which was obtained from samples of nitrile-contaminated soil collected in the Saratov Region (Russian Federation). This genomic resource will support the further development of biocatalysts for the inexpensive and green production of acrylic monomers.

Draft Genome Sequence of Rhodococcus qingshengii Strain PN_19, Isolated from a Moribund Individual of Pinna nobilis in Sardinia, Italy.

ABSTRACTDuring an epidemiological survey that aimed to discover the causes for the mass mortality of Pinna nobilis, a strain of Rhodococcus was found in a moribund individual. Here, we report its 7,037,134-bp draft genome sequence, which, after the annotation and genome survey, was identified as belonging to Rhodococcus qingshengii PN_19.

Complete Genome Sequence of Rhodococcus qingshengii Strain CL-05, Isolated from Concrete.

Here, we report the complete genome sequence of Rhodococcus qingshengii strain CL-05, which was isolated from pavement concrete in Newark, Delaware. The genome consists of a 6.29-Mbp chromosome and one plasmid (123,183 bp), encodes a total of 5,859 predicted proteins, and has a GC content of 62.5%.

Toxicity evaluation of the metabolites derived from the degradation of phenanthrene by one of a soil ubiquitous PAHs-degrading strain Rhodococcus qingshengii FF

Rhodococcus qingshengii strain FF is a soil ubiquitous strain that has a high polycyclic aromatic hydrocarbons (PAHs) biodegradation capability. In this work, phenanthrene was used as a PAH model compound. The accumulated pattern of the metabolites of phenanthrene by strain FF was investigated, and their toxicity to Vibrio fischeri, effect on microbiota diversity of farmland soil and influence on seed of wheat were evaluated. Total of 29 main intermediates were observed for the phenanthrene degradation process. Pyrogallol was the predominant accumulated metabolite, and 59% of the accumulated metabolites were oxygen-containing PAHs that have only one benzene ring. The acute toxicity assessment showed the accumulated metabolites in later phase were more toxic to Vibrio fischeri. Microbe and wheat seed response to the different stages of phenanthrene metabolites indicated pollution significantly decreased microbial richness and evenness of farmland soil and lower germinal length, root length or root number of wheat seed. These results indicated that not only the elimination of PAHs, but also the easily accumulated metabolites produced during the PAHs degradation process should be paid enough attention. The comprehensive evaluation of toxicity during the degradation process would provide useful information for the use of microbe-orientated strategies in PAHs bioremediation.

Potential effects of Rhodococcus qingshengii strain djl-6 on the bioremediation of carbendazim-contaminated soil and the assembly of its microbiome

As a widely used fungicide, the environmental fate of carbendazim and its residues in agricultural products have caused great concern. However, its effects on soil microbial communities are largely unknown. Herein, we used high-throughput sequencing to reveal the effects of high and low dose of carbendazim and its degrading strain, Rhodococcus qingshengii strain djl-6, on the composition, diversity, and interrelationship of soil bacterial and fungal communities in short- and medium-term under laboratory conditions. The results showed that carbendazim exhibited an increased negative impact on bacterial communities and reduced the proportion of dominant fungal phylum Ascomycota during a 14-day incubation period. Only the impacts of low-dose carbendazim (2 mg·kg−1 dry soil) on fungal community were weakened. Network analysis showed that carbendazim increased the connectivity and modularity of microbial co-occurrence networks. Strain djl-6 exhibited good potential for bioremediation of carbendazim-contaminated soils. Moreover, it driven the assembly of potential carbendazim-degrading consortia from indigenous microbial communities; and members of the genera Arthrobacter, Bacillus, Brevundimonas, Lysinibacillus, Massilia, Mycobacterium, Paenibacillus, and Pseudarthrobacter might be participated in the degradation of carbendazim. Taken together, our study provides a relatively comprehensive understanding of the effects of carbendazim and its degrading strain djl-6 on soil microbial communities.

Genomic and phenotypic analysis of siderophore-producing Rhodococcus qingshengii strain S10 isolated from an arid weathered serpentine rock environment

The success of members of the genus Rhodococcus in colonizing arid rocky environments is owed in part to desiccation tolerance and an ability to extract iron through the secretion and uptake of siderophores. Here, we report a comprehensive genomic and taxonomic analysis of Rhodococcus qingshengii strain S10 isolated from eathered serpentine rock at the arid Khalilovsky massif, Russia. Sequence comparisons of whole genomes and of selected marker genes clearly showed strain S10 to belong to the R. qingshengii species. Four prophage sequences within the R. qingshengii S10 genome were identified, one of which encodes for a putative siderophore-interacting protein. Among the ten non-ribosomal peptides synthase (NRPS) clusters identified in the strain S10 genome, two show high homology to those responsible for siderophore synthesis. Phenotypic analyses demonstrated that R. qingshengii S10 secretes siderophores and possesses adaptive features (tolerance ofup to 8% NaCland pH 9) that should enable survival in its native habitat within dry serpentine rock.

Immobilization of Rhodococcus qingshengii strain FF on the surface of polyethylene and its adsorption and biodegradation of mimic produced water

Low pH and high salinity characteristic of produced water (PW) posed a big challenge for the direct biological treatment. The immobilization of R. qingshengii strain FF, which degraded petroleum effectively under low pH, and application of immobilized R. qingshengii strain FF in treating mimic PW was studied in this work. The immobilization of R. qingshengii strain FF on the surface of polyethylene foam (PEF), one type of waste packaging materials, was optimized using the response surface methodology. Under optimum conditions, cell density of R. qingshengii strain FF immobilized on the surface of PEF reached 388 mg (cells)/g(PEF). In addition, a few factors, including hydraulic retention time (HRT), pH and salinity, were studied for treating mimic PW using immobilized R. qingshengii strain FF. The result of this study demonstrated that TPH degradation efficiency of PW by immobilized R. qingshengii strain FF reached above 90% when HRT was longer than 8 h. Weak acid and high salinity conditions only moderately decreased TPH. Asphalt, alkanes and aromatic hydrocarbon contained in petroleum can be degraded to some extent. These results indicated that immobilized R. qingshengii strain FF can be used as a highly efficient strain which could be used in biological treatment of real PW.

Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8.

Rhodococcus strain IGTS8 is the most extensively studied model bacterium for biodesulfurization of fossil fuels via the non–destructive sulfur–specific 4S pathway. This strain was initially assigned to Rhodococcus rhodochrous and later to Rhodococcus erythropolis thus making its taxonomic status debatable and reflecting the limited resolution of methods available at the time. In this study, phylogenomic analyses of the whole genome sequences of strain IGTS8 and closely related rhodococci showed that R. erythropolis and Rhodococcus qingshengii are very closely related species, that Rhodococcus strain IGTS8 is a R. qingshengii strain and that several strains identified as R. erythropolis should be re-classified as R. qingshengii. The genomes of strains assigned to these species contain potentially novel biosynthetic gene clusters showing that members of these taxa should be given greater importance in the search for new antimicrobials and other industrially important biomolecules. The plasmid-borne dsz operon encoding fossil fuel desulfurization enzymes was present in R. qingshengii IGTS8 and R. erythropolis XP suggesting that it might be transferable between members of these species.

De Novo Genome Assembly of a Plant-Associated Rhodococcus qingshengii Strain (RL1) Isolated from Eruca sativa Mill. and Showing Plant Growth-Promoting Properties.

Rhodococcus qingshengii RL1 was isolated from surface-sterilized leaves of Eruca sativa Mill. and shows plant growth-promoting (PGP) properties. The de novo genome assembly consists of one chromosome with 6,253,838 bp and two plasmids with 144,038 bp and 448,745 bp. Many genes could be identified reflecting its PGP potential.

Characterization of trehalose lipids produced by a unique environmental isolate bacterium Rhodococcus qingshengii strain FF.

The aim of this study was to elucidate the chemical properties and applications of trehalose lipids produced by Rhodococcus qingshengii strain FF and optimize its production yield. Strain FF was identified as R. qingshengii. It was observed to produce biosurfactants in the presence of n-hexadecane. The biosurfactants were identified as the mixture of trehalose triesters and trehalose tetraesters, mainly consisting of TrehC12 C3 C6 C12 :10, TrehC11 C8 C6 :6, TrehC11 C6 C4 :5 and TrehC6 C4 C6 :5 based on the analysis of thin layer chromatography, Fourier transform infrared and flight tandem mass spectrometry. The best carbon source and nitrogen source for producing trehalose lipids was the mixture of n-hexadecane and oleic acid (m:m=1:1) and the organic nitrogen, urea. Under this condition, the production of trehalose lipids could reach 7·97gl-1 . The crude trehalose lipids showed extremely high surface-active properties and were proven to promote the degradation of naphthalene. The trehalose lipids produced by R. qingshengii strain FF exhibited high surfactant activity under various conditions and were proven to promote the degradation of naphthalene. Rhodococcus qingshengii strain FF is a potential candidate for bioremediation. The trehalose lipids might be used as unique biosurfactants in cosmetic industries, biological formulations and other applications.

BIOACTIVITIES OF THE ETHYL ACETATE EXTRACT OF RHODOCOCCUS QINGSHENGII STRAIN BJC15-A38 AN ENDOPHYTE OF AZADIRACHTA INDICA A. JUSS

Objective: This study evaluated the antidiabetic activities of the ethyl acetate-methanol (4:1) extract (EA) of Rhodococcus qingshengii strain BJC15-A38 supernatant.Methods: In vitro alpha-amylase and alpha-glucosidase inhibitory assays, were used to determine the antidiabetic activity of EA (100, 250, 500, 750 and 1000 μg/ml). Also, the total phenol content of the extract was determined, followed by understanding the mode of α-amylase inhibition.Results: The crude extract from Azadirachta indica A. Juss. endophytic actinomycete Rhodococcus qingshengii strain BJC15-A38 was found to have significant inhibition against α-amylase (IC50 = 65.93 µg/ml) and α-glucosidase (IC50 = 929.56 µg/ml). The total phenol content of the crude was found to be 97.25±6.47 and 15.40±0.43 mg/g of the extract in terms of catechol and gallic acid equivalents respectively. Purification of the extract was carried out using silica gel column chromatography. Kinetic analysis revealed the mixed competitive with mixed competitive of inhibition towards α-amylase.Conclusion: The findings suggest that the extract of Rhodococcus qingshengii strain BJC15-A38 possesses antidiabetic effects.